Direct quantification of loop interaction and π-π stacking for G-quadruplex stability at the submolecular level

Area of Science:

• Molecular Biology
• Biophysics
• Medicinal Chemistry

Background:

• DNA G-quadruplexes have critical cellular functions, necessitating small molecules to modulate their activity.
• Limited understanding of how submolecular elements like loops and G-quartets influence G-quadruplex stability hinders the development of effective small-molecule binders.

Purpose of the Study:

• To dissect the contributions of loop interactions versus G-quartet stacking to the mechanical stability of human telomeric G-quadruplexes.
• To provide insights for designing improved G-quadruplex-interacting molecules.

Main Methods:

• Utilized click chemistry to attach pulling handles to guanines within the G-quadruplex structure.
• Employed mechanical unfolding techniques to measure stability contributions from different structural elements.
• Investigated the effect of stacking ligands on G-quadruplex mechanical stability.

Main Results:

• Loop interactions were found to contribute more significantly to G-quadruplex stability than G-quartet stacking.
• Stacking ligands reduced loop interactions, leading to uniform mechanical stability across G-quartets.
• Submolecular dissection provided a less disruptive method for evaluating individual structural domains compared to traditional mutation-based approaches.

Conclusions:

• Loop interactions are a dominant factor in human telomeric G-quadruplex stability.
• This detailed understanding can guide the rational design of novel G-quadruplex-targeting therapeutics.
• Mechanical unfolding of G-quadruplexes offers a valuable complementary approach to traditional biochemical methods.